Re: [gmx-users] Free energy between residues

2012-06-28 Thread lloyd riggs
for GROMACS users > Betreff: Re: [gmx-users] Free energy between residues > > > On 6/28/12 6:51 AM, Steven Neumann wrote: > > On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul > wrote: > >> > >> > >> On 6/28/12 6:33 AM, Steven Neuma

Re: [gmx-users] Free energy between residues

2012-06-28 Thread Justin A. Lemkul
On 6/28/12 6:51 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From

Re: [gmx-users] Free energy between residues

2012-06-28 Thread Steven Neumann
On Thu, Jun 28, 2012 at 11:42 AM, Justin A. Lemkul wrote: > > > On 6/28/12 6:33 AM, Steven Neumann wrote: >> >> On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: >>> >>> Dear Steven, >>> >>> Where are you working? >> >> >> I work in UK, London. Why are you asking? >> >> >>> >From my experience

Re: [gmx-users] Free energy between residues

2012-06-28 Thread Justin A. Lemkul
On 6/28/12 6:33 AM, Steven Neumann wrote: On Thu, Jun 28, 2012 at 11:20 AM, lloyd riggs wrote: Dear Steven, Where are you working? I work in UK, London. Why are you asking? >From my experience the g_energy -fee only gives a free enrgy estimate for the whole system, so one has to pull

Re: [gmx-users] Free energy between residues

2012-06-28 Thread Steven Neumann
ulombic) and then can get the effective potential Ueff=-kTln Sincerely, > > Stephan Watkins > > Original-Nachricht >> Datum: Thu, 28 Jun 2012 09:28:09 +0100 >> Von: Steven Neumann >> An: Discussion list for GROMACS users >> Betreff: [gmx-users] F

Re: [gmx-users] Free energy between residues

2012-06-28 Thread lloyd riggs
imates for a specific set, please let me know this would be valuable >to me. Sincerely, Stephan Watkins Original-Nachricht > Datum: Thu, 28 Jun 2012 09:28:09 +0100 > Von: Steven Neumann > An: Discussion list for GROMACS users > Betreff: [gmx-users] Free energy b

[gmx-users] Free energy between residues

2012-06-28 Thread Steven Neumann
Dear Gmx Users, I want to obtain the free energy difference between the pair of residues in my protein chain with respect to thheir distance. Would combinbation: 1) g_dist - distances between two groups during the simulation time 2) g_energy -fee (DelatG - with energy groups I am interested in s